Glycosylation is a prevalent form of post translational modification, believed to occur on over 50% of human proteins. Homogeneous forms of glycoproteins are essential for developing an understanding of how activity is mediated at a structural level. As biological origins of glycoproteins give rise to complex mixtures of glycoforms, homogeneous glycoprotein production has become an important goal. As chemical protein synthesis is often limited to sequences of 30-50 residues, access to large native glycoproteins is currently restricted to fragment based approaches. Protein semi-synthesis enables the preparation of larger proteins which can be difficult to obtain through chemical synthesis alone. Consequently, a general semi-synthetic strategy towards N-glycoproteins has been proposed and demonstrated on Interferon-β-1 (IFNβ), a 166 residue glycoprotein. A three fragment strategy was designed, relying on the chemical synthesis of a short glycopeptide segment and recombinant expression of the two flanking domains. Homogeneity was established through the chemical synthesis of a glycopeptide containing a natively linked N-acetylglucosamine (GlcNAc), also enabling the selective transfer of complex oligosaccharides. After cloning and expression, the recombinant fragments were functionalised to allow assembly of the protein using Native Chemical Ligation. These desired protein modifications were achieved through the application of highly chemoselective reactions. These reactions were also applied towards the generation of N-glycopeptides compatible with the ligation strategy. Further to this, existing methods enabling the direct synthesis of functionalised N-glycopeptides were also explored. After glycopeptide synthesis, endoglycosidase A enabled the transfer of oligosaccharides to the N-acetylglucosamine motif. This has allowed the preparation of the desired IFNβ glycopeptide as well as a glycosylated variant of glucagon like peptide-1. To expand the utility of endoglycosidase methodology, a novel sugar nucleotide was synthesised to facilitate the incorporation of a sialyl galactose mimic onto N-glycans. The resulting oligosaccharides may serve as novel substrates for endoglycosidases in the preparation of N-glycoprotein mimics.

Cum animum plantis intendere, earumque physiologiae operam haud parvam dare non dedignentur feientiae cultores, pauea plantarum vitam spectantia tradere in animum induxi. Quo vera rem diluddius exponerem, vitam animalium pauds primum attingere decrevi; dein motus quosdam plantarum insignes memorabo; postremo de earum vi vitae sedeque breviter differam.

Many important biogeochemical processes that occur in marine sediments are intimately linked to pH dependent processes, but surprisingly little is known about the details of the pH profiles generated. This is mainly due to the difficulty of obtaining samples and measuring representative profiles. Such profiles have previously been determined using glass-membrane micro-electrodes, but this is slow and electrodes easily break in harsh sediments (insertion is “blind”). Profiles have also been measured using fluorescent dye-based sensors, but their handling needs special light sources and filters and sensor membrane preparation is quite complex, which has restricted its use to laboratory studies. A simple optical pH sensor has been developed for this application by immobilising bromothymol blue in a PVC membrane. This device responds in a pH range suitable for marine sediments. The sensor is simple to use, the dye does not leach and it gives a visible colour readout so when photographed, the pictures can be used to extract Red Green Blue values and converting them to colour index values representing the sensor colour. This can be related to pH via a colour index v pH calibration using standard buffers or seawater by bubbling CO2. The sensor responds reasonably quickly and can be used for multiple cycles. Sensor strips have been attached to transparent plastic probes with a Nytran diffusion membrane added to provide a white background to stop interference from the colour of sediments. Preliminary tests have been carried out by inserting these probes in sediment cores (in the lab and aboard the RVs Endeavour, Discovery and Prince Madog), and also in the field at Stiffkey salt marsh, in order to measure vertical pH profiles. This has provided promising results. Seasonal profiles at Stiffkey have been taken, recording pH values ranging from 5-8. The sensors have been adapted for use with a Sediment Profile Imagery (SPI) system, to map the pH profile of marine sediments rapidly in-situ using various survey approaches.

The widespread development of bacterial resistance to antibiotics is an ongoing process which represents a growing problem for modern medicine. Vancomycin is used as a drug of last resort against methicillin-resistant Staphylococcus aureus (MRSA), but the increasing prevalence of vancomycin-resistant bacteria has intensified the search for new antibiotics. The introductory chapter of this thesis presents an overview of publications reporting the synthesis of glycopeptide analogues and derivatives in the last decade, highlighting the successful approaches which have brought new pharmaceutical drugs to the market. The results and discussion section of this work focusses first on the synthesis of a triaryl biether structure, which is a common feature of the glycopeptide antibiotic family and represents the beginning of a versatile synthetic approach towards natural products like orienticin C and vancomycin. The second discussion chapter describes the development of an asymmetric organocatalytic aza-Darzens aziridination protocol using diazopeptides and amino acid imines as substrates. A structurally diverse range of peptide aziridines are reported in yields and diastereoselectivity of up to 99%. It is anticipated that the remote asymmetric induction methodology described in this thesis will be applicable not only to the synthesis of novel glycopeptide antibiotics and other peptide-based pharmaceutical compounds, but also to the more general asymmetric synthesis of natural and unnatural amino acids.

The first part of this thesis is concerned with the attachment of subphthalocyanines to quantum dots. The macromolecule was chosen as encapsulant due to its perfect curvature and interesting optical properties. CdSe quantum dots are well-known materials with size-dependent properties that makes them unique. Hence, some subphthalocyanines bearing functional groups with affinity for the CdSe surface were synthesised by means of cross-coupling reactions. Small nanoparticle size (2.6 nm) quantum dots have been synthesised, capped with a layer of oleic acid molecules that confers them stability, and characterised by means of UV-Vis, emission and NMR spectroscopies. The original ligands were replaced by ligand exchange processes monitored by 1HNMR spectroscopy. The experiments consist of titrations of CdSe-OA solutions with known concentrations of the new ligand. In this work, titrations using 3-ethynylpyridine, benzyl alcohol and phenylacetic acid have been performed. Parallel results in our group, involving the herein synthesised subphthalocyanine bearing pyridyl – groups, towards the attachment to the nanoparticle’s surface are also described. Subphthalocyanine bearing three carboxylic acids is demonstrated to be the most promising candidate for this project. However, attempts to synthesise such a molecule by direct approach strategies were unsuccessful. Experiments with sodium periodate-subphthalocyanine conjugates gave promising and encouraging results, opening the possibility of accessing subphthalocyanines with carboxylic acid groups by means of deprotecting silyl groups. The second part of this thesis is based on the results obtained towards the first syntheses of hybrid structures whose structure lies between subphthalocyanines and subporphyrins, SubTriBenzoDiAzaPorphyrins (SubTBDAPs). The key intermediates are aminoisoindolene precursors that provide the methine bridge, and substitution with the meso-phenyl ring. Boron trichloride has been used in a two-step, one-pot reaction in a preliminary strategy to give access to the hybrids. However, trialkoxyborates are the preferred boron source; they provide the apical substituent, as well as act as Lewis acid and template. The latter synthesis is versatile and gives modest yields and highly pure materials, but most importantly allows control over the apical and the meso-substituents in one single step. The new hybrids exhibit interesting optical and rotational characteristics that have been fully investigated by means of UV-Vis, emission, NMR spectroscopies, variable temperature experiments and mass spectrometry. In this work the first crystal structures elucidated for a wide range of new hybrids are also presented.

The theory of quantum electrodynamics is employed in the description of linear and nonlinear optical effects. We study the effects of using a two energy level approximation in simplifying expressions obtained from perturbation theory, equivalent to truncating the completeness relation. However, applying a two-level model with a lack of regard for its domain of validity may deliver misleading results. A new theorem on the expectation values of analytical operator functions imposes additional constraints on any atom or molecule modelled as a two-level system. We introduce measures designed to indicate occasions when the two-level approximation may be valid. Analysis of the optical angular momentum operator delivers a division into spin and orbital parts satisfying electric-magnetic democracy, and determine a new compartmentalisation of the optical angular momentum. An analysis is performed on the recently rediscovered optical chirality, and its corresponding flux, delivering results proportional to the helicity and spin angular momentum in monochromatic beams. A new polarisation basis is introduced to determine the maximum values that an infinite family of optical helicity- and spin- type measures may take, and disproves recent claims of ‘superchiral light’. A theoretical description of recent experiments relate helicity- and spin- type measures to the circular differential response of molecules, and show that nodal enhancements to circular dichroism relate only to photon number-phase uncertainty relation and do not signify ‘superchiral’ regions. The six-wave mixing of optical vortex input, in nonlinear media, demonstrates the quantum entanglement of pairs of optical vortex modes. The probability for each possible output pair displays a combinatorial weighting, associated with Pascal’s triangle. A quantum electrodynamic analysis of the effect of a second body on absorption can be extended by integrating over all possible positions of the mediator molecules, modelling a continuous medium. This provides links with both the molecular and bulk properties of materials.

Hydrogenase enzymes are nature’s catalysts for hydrogen production and uptake. Understanding how they work may lead to new materials as alternatives for precious metals currently used in H2-utilizing fuel and producer cells. Work described in this thesis focuses on synthetic mimics of the active site of [Fe Fe]-hydrogenases and explores their reactivity towards protons and electrons. Chapter 1 gives a brief overview of the chemistry taking place in hydogenase enzymes with a particular focus on the [Fe Fe]-hydrogenase. The evolution of synthetic models mimicking the structure and function of the enzyme from the late 1990s to the current state of the art is discussed. Chapter 2 describes synthesis of the first {2Fe3S} hydride together with new active site mimics in which bulky substituents are incorporated into the dithiolate bridgehead. A comprehensive examination of their structural features and spectroscopic properties is provided. Chapter 3 reports extensive stopped-flow UV-vis, IR and electrochemical studies for a range of subsite models exploring the relationship between the structure and the reactivity towards protons. It is shown that there is a direct linear free energy relationship between the activation energy for protonation and the energy level of the HOMO. Chapter 4 describes the first characterisation of paramagnetic (mixed-valence) Fe(I)(μ-H)- Fe(II) species which is implicated in metallo-sulfur enzymes as an intermediate in electrocatalytic H2 evolution. An unprecedented super reduced state is detected and characterised using a custom-built spectroelectrochemical cell. Chapter 5 shows how muon spectroscopy may provide a new approach for exploring metallo-hydride chemistry. Future avenues of research in the field of [Fe Fe] chemistry arising from the work described in this thesis are also briefly discussed.

Soils are frequently analysed by forensic laboratories by comparing a suspect sample to an especially collected control sample. As yet, they cannot be compared to a central database, unless the area in question has already been identified; with the use databases being highly contested within the field of forensic geosciences. There is a need for a method of soil profiling that allows an unknown sample to be tested and assigned a quantitative likelihood that it originated from a given region. Spatial models can then be created using geographical information systems to house multiple datasets and be used to map soils across geographical areas. Generally, the more variables available with which to compare items, the greater the certainty a forensic analyst can have when asserting their similarity; this applies to geological materials. Equally, soil profiling methods can be used to exclude soil samples from each other or an area. This research involves a number of chemical and biological profiling methods that have been used to build up a unique signature for soils from different locations across Norfolk. All analyses have been carried out on a single source sample. 87Sr/86Sr ratios have been measured using MC-ICP-MS, and trace element concentrations measured using ICP-MS. The 87Sr/86Sr ratios are significantly different at each of the sample locations; although there is some variation in the replicates collected at each location this variation is smaller than the regional variation. The correlation between the isotope chemistry of the topsoil and the underlying geology is poor, indicating that other sources such as land-use, vegetation cover and additions to the soil contribute to the 87Sr/86Sr. Therefore, trace element concentrations have been used to spatially discriminate samples and to investigate the effect of fertilisers on the elemental composition of the topsoil. The biological techniques used to aid discrimination are soil DNA analysis using the chloroplast-located matK gene and MALDI-ToF-MS, palynology and the creation of Norfolk vegetation maps showing all of the plant species recorded in the area; each additional independent dataset allows for an increasing signature of each sample to be built up which can be used for assessing similarity or exclusionary purposes.

This project applies superfluid helium droplets in two big areas: spectroscopy and nanoparticles formation. Helium droplets, consisted of more than 103 helium atoms, provide a non-friction and very cold (~0.37 K) environment for clusters/nanoparticles growth, which offers unique advantages as a medium in applications of both spectroscopy and nanostructures formation. By sequentially adding NaCl and water molecules, the dissolution process of NaCl in water can be experimentally studied for the first time. This is achieved by recording the infra-red spectra of NaCl(H2O)n (1 ≤ n ≤ 7) complexes in O-H stretching region in combination with ab initio calculations. In particular, two bands have been assigned to dissolution of NaCl in water. The existence of quantum vortices in helium droplets has been firmly evident from spherical Ag nanoparticles formed in a chain. Quantum vortices provide a new route for the formation of one-dimensional nanostructures, which has been exploited in the fabrication of novel nanowires. Finally the pioneering work on the fabrication of both antiferromagnetic and ferromagnetic nanomaterials is reported for the first time, taking Cr and Ni as examples respectively. It is found that we can force ferromagnetic ordering in magnetic materials in superfluid helium. In particular, antiferromagnetic chromium has been discovered to convert to ferromagnetic, and the magnetism of ferromagnetic materials can have hugely enhanced magnetic moments that are close to the theoretical limit. This will have potential for applications in biomedical science, data storage and energy efficient technologies in the longer term.

Pyrrole/imidazole polyamides are a class of molecules that bind to double-stranded DNA with nanomolar binding affinity, enabling the disruption of transcription factor binding to their target DNA sequence. Polyamides have previously demonstrated the ability to regulate gene expression in vitro and in vivo through inhibition of transcription factor binding. One of the major limitations of polyamide research is the lack of streamlined access to libraries of these compounds. This thesis describes optimized synthetic routes for the preparation of hairpin polyamides. Efforts were made to improve access to monomer units, in addition to the development of a set of standard solid-phase polyamide synthesis conditions, which allowed consistent preparation of hairpin polyamides in high yields and purity. Further to this, a novel fragment-based convergent synthesis has been established to afford hairpin polyamides with crude purities of 85-92%, and with a 3-fold increase in isolated yields compared to existing approaches. Polyamides were prepared to bind to DNA sequences located within the transcription factor binding sites in the promoter region of the human ApoB gene, a protein known to be causative of cardiovascular disease. In cellulo analysis of these polyamides using HepG2 cells revealed their localization within the nucleus, a prerequisite for successful pre-transcriptional regulation. It was also discovered that targeting the C/EBP and HNF4 transcription factor binding sites with DNA-binding polyamides resulted in toxicity before concentrations were sufficient for down-regulation of the ApoB gene. Polyamides have also been designed to inhibit FUR protein/DNA interactions in the staphylococcus aureus pathogen, with the aim to disrupt homeostasis. Initial results have concluded the tight binding of these polyamides, and biological studies are in progress to validate this as a viable therapeutic avenue.